variation Namespace Reference

Classes
class	CHgvsParser
class	CVariationUtil
class	SFastLocSubtract
	Note: this is strand-agnostic. More...

Functions
	USING_SCOPE (objects)
CVariantPlacement &	SetFirstPlacement (CVariation &v)
void	SetComputational (CVariation &variation)
bool	SeqsMatch (const string &query, const char *text)
CRef< CSeq_loc >	FindSSRLoc (const CSeq_loc &loc, const string &seq, CScope &scope)
void	RepackageAssertedSequence (CVariation &vr)
void	AdjustMoltype (CVariation &vr, CScope &scope)
template<typename T >
T	AdjustHgvsCoord (T val, TSeqPos offset, bool adjust)
bool	IsPureFuzzPoint (const CSeq_point &p)
CSeq_id_Handle	GetUniquePrimaryTranscriptId (CBioseq_Handle &bsh)
bool	IsLRG (CBioseq_Handle &bsh)
int	GetDeltaLength (const CDelta_item &delta, int loc_len)
CVariation_inst::EType	GetDelInsSubtype (int del_len, int ins_len)
string	Ncbieaa2HgvsAA (const string &prot_str)
bool	IsMitochondrion (CBioseq_Handle bsh)
bool	ContainsAnyFuzz (CConstRef< CVariantPlacement > p)
static CRef< CVariationException >	CreateException (const string &message, CVariationException::ECode code=static_cast< CVariationException::ECode >(0))
template<typename T >
static void	ChangeIdsInPlace (T &container, sequence::EGetIdType id_type, CScope &scope)
static bool	ValidExonTerminal (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, TSeqPos exon_anchor_pos, int offset_pos)
static int	GetFuzzSign (const CInt_fuzz &fuzz, int loc_sign)
static bool	ValidExonTerminals (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, const CVariantPlacement &p)
static void	SwapLtGtFuzz (CInt_fuzz &fuzz)
static void	ApplyOffsetFuzz (CSeq_loc &loc, const CInt_fuzz &offset_fuzz, bool is_start)
static CRef< CSeq_align >	CreateSplicedSeqAlignFromFeat (const CSeq_feat &rna_feat)
template<typename T >
static bool	ContainsIupacNaAmbiguities (const T &obj)
static bool	IsRightPartial (CBioseq_Handle bsh)
static string	Translate (const string &nuc_str, bool is_mito)
CVariation_inst::EType	CalcInstTypeForAA (const string &prot_ref_str, const string &prot_delta_str)
static CVariantProperties::TEffect	CalcEffectForProt (const string &prot_ref_str, const string &prot_delta_str)
static CVariationUtil::TSOTerms	CalcSOTermsForProt (TSignedSeqPos nuc_delta_len, const string &prot_ref_str, const string &prot_variant_str)
static bool	Contains (const CSeq_loc &a, const CSeq_loc &b, CScope *scope)
static CRef< CVariation >	CreateUnknownProtConsequenceVariation (const CVariantPlacement &nuc_p, const CSeq_feat &cds_feat, bool is_frameshifting, CScope &scope)
static size_t	GetCommonPrefixLen (const string &a, const string &b)
static size_t	GetCommonSuffixLen (const string &a, const string &b)
static bool	HasProblematicExceptions (const CSeq_feat &cds_feat)
static bool	Equals (const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)
static bool	IsRefSeqGene (const CBioseq_Handle &bsh)
static set< int >	GetFocusLocusIDs (const CBioseq_Handle &bsh)
CRef< CVariation >	InheritParentAttributes (const CVariation &child, const CVariation &parent)
static CRef< CDelta_item >	CreateDeltaForOffset (int offset, const CInt_fuzz *fuzz)
static int	GetSignedOffset (const CDelta_item &delta)
static const CInt_fuzz *	GetFuzz (const CDelta_item &delta)

Function Documentation

AdjustHgvsCoord()

template<typename T >

T variation::AdjustHgvsCoord	(	T	val,
		TSeqPos	offset,
		bool	adjust
	)

Definition at line 501 of file hgvs_parser2.cpp.

References offset, T, and val.

Referenced by variation::CHgvsParser::x_abs_pos().

AdjustMoltype()

void variation::AdjustMoltype	(	CVariation &	vr,
		CScope &	scope
	)

Definition at line 341 of file hgvs_parser2.cpp.

References Begin(), CVariantPlacement_Base::eMol_rna, CSeq_loc::GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), CVariantPlacement_Base::IsSetMol(), and CVariantPlacement_Base::SetMol().

Referenced by variation::CHgvsParser::x_root().

ApplyOffsetFuzz()

static void variation::ApplyOffsetFuzz ( CSeq_loc &  loc, const CInt_fuzz &  offset_fuzz, bool  is_start  )

static

Definition at line 303 of file variation_util2.cpp.

References CSerialObject::Assign(), CInt_fuzz_Base::eLim_unk, eNa_strand_minus, CSeq_loc::GetStrand(), CInt_fuzz_Base::IsRange(), CSeq_loc::SetInt(), CInt_fuzz_Base::SetLim(), SwapLtGtFuzz(), and CInt_fuzz_Base::Which().

Referenced by variation::CVariationUtil::s_ResolveIntronicOffsets().

CalcEffectForProt()

static CVariantProperties::TEffect variation::CalcEffectForProt ( const string &  prot_ref_str, const string &  prot_delta_str  )

static

Definition at line 2012 of file variation_util2.cpp.

References CVariantProperties_Base::eEffect_missense, CVariantProperties_Base::eEffect_stop_gain, CVariantProperties_Base::eEffect_stop_loss, CVariantProperties_Base::eEffect_synonymous, and i.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

CalcInstTypeForAA()

CVariation_inst::EType variation::CalcInstTypeForAA	(	const string &	prot_ref_str,
		const string &	prot_delta_str
	)

Definition at line 1997 of file variation_util2.cpp.

References CVariation_inst_Base::eType_del, CVariation_inst_Base::eType_ins, CVariation_inst_Base::eType_prot_missense, CVariation_inst_Base::eType_prot_nonsense, CVariation_inst_Base::eType_prot_other, CVariation_inst_Base::eType_prot_silent, NStr::Find(), and NPOS.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

CalcSOTermsForProt()

static CVariationUtil::TSOTerms variation::CalcSOTermsForProt ( TSignedSeqPos  nuc_delta_len, const string &  prot_ref_str, const string &  prot_variant_str  )

static

Definition at line 2031 of file variation_util2.cpp.

References variation::CVariationUtil::eSO_frameshift_variant, variation::CVariationUtil::eSO_inframe_indel, variation::CVariationUtil::eSO_missense_variant, variation::CVariationUtil::eSO_stop_gained, variation::CVariationUtil::eSO_stop_lost, variation::CVariationUtil::eSO_synonymous_variant, i, max(), and r().

Referenced by variation::CVariationUtil::TranslateNAtoAA().

ChangeIdsInPlace()

template<typename T >

static void variation::ChangeIdsInPlace ( T &  container, sequence::EGetIdType  id_type, CScope &  scope  )

static

Definition at line 112 of file variation_util2.cpp.

References Begin(), eGetId_ForceAcc, eGetId_ForceGi, GetId(), CSeq_id_Handle::GetSeqId(), and NCBI_USER_THROW.

Referenced by CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::CCdregionIndex::Get(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), variation::CVariationUtil::CVariantPropertiesIndex::GetLocationProperties(), variation::CVariationUtil::RemapToAnnotatedTarget(), variation::CVariationUtil::TranslateNAtoAA(), variation::CVariationUtil::x_CreateUnknownVariation(), variation::CVariationUtil::x_InferNAfromAA(), and variation::CVariationUtil::x_Remap().

Contains()

static bool variation::Contains ( const CSeq_loc &  a, const CSeq_loc &  b, CScope *  scope  )

static

Definition at line 2259 of file variation_util2.cpp.

References a, CSeq_loc::Assign(), b, Compare(), eContains, fCompareOverlapping, and CSeq_loc::ResetStrand().

Referenced by CSimpleDesktopItem::FindItem(), CCompositeDesktopItem::FindItem(), CNoFocusBitmapButton::OnMotion(), CNoFocusBitmapButton::OnMouseUp(), variation::CVariationUtil::TranslateNAtoAA(), and CwxTableListCtrl::x_ShowTooltip().

ContainsAnyFuzz()

bool variation::ContainsAnyFuzz

(

CConstRef< CVariantPlacement >

p

)

Definition at line 823 of file hgvs_writer2.cpp.

References Begin(), false, and true.

Referenced by variation::CHgvsParser::x_AsHgvsInstExpression().

ContainsIupacNaAmbiguities()

template<typename T >

static bool variation::ContainsIupacNaAmbiguities ( const T &  obj )

static

Definition at line 768 of file variation_util2.cpp.

References Begin(), CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacna(), CSeq_data_Base::IsIupacna(), and ITERATE.

Referenced by variation::CVariationUtil::AttachSeq(), and variation::CVariationUtil::CheckAmbiguitiesInLiterals().

CreateDeltaForOffset()

static CRef<CDelta_item> variation::CreateDeltaForOffset ( int  offset, const CInt_fuzz *  fuzz  )

static

Definition at line 4405 of file variation_util2.cpp.

References abs, delta(), CDelta_item_Base::eAction_offset, and offset.

Referenced by variation::CVariationUtil::s_AddInstOffsetsFromPlacementOffsets().

CreateException()

static CRef<CVariationException> variation::CreateException ( const string &  message, CVariationException::ECode  code = static_cast<CVariationException::ECode>(0)  )

static

Definition at line 97 of file variation_util2.cpp.

Referenced by variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::CheckAmbiguitiesInLiterals(), variation::CVariationUtil::CheckPlacement(), CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::Remap(), and variation::CVariationUtil::x_Remap().

CreateSplicedSeqAlignFromFeat()

static CRef<CSeq_align> variation::CreateSplicedSeqAlignFromFeat ( const CSeq_feat &  rna_feat )

static

Definition at line 603 of file variation_util2.cpp.

References CSeq_loc_CI::eEmpty_Skip, eNa_strand_plus, CSeq_loc_CI::eOrder_Biological, CSpliced_seg_Base::eProduct_type_transcript, CSeq_align_Base::eType_other, GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), GetStrand(), NULL, CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetGenomic_id(), CSpliced_seg_Base::SetGenomic_strand(), CSpliced_seg_Base::SetProduct_id(), CSpliced_seg_Base::SetProduct_strand(), CSpliced_seg_Base::SetProduct_type(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType().

Referenced by variation::CVariationUtil::RemapToAnnotatedTarget().

CreateUnknownProtConsequenceVariation()

static CRef<CVariation> variation::CreateUnknownProtConsequenceVariation ( const CVariantPlacement &  nuc_p, const CSeq_feat &  cds_feat, bool  is_frameshifting, CScope &  scope  )

static

Definition at line 2286 of file variation_util2.cpp.

References ChangeIdsInPlace(), CreateException(), CVariationException_Base::eCode_inconsistent_consequence, eGetId_ForceAcc, CSeq_loc_Mapper_Base::eLocationToProduct, CVariationMethod_Base::eMethod_E_computational, CVariantPlacement_Base::eMol_protein, CSeq_loc_Mapper_Base::eProductToLocation, variation::CVariationUtil::eSO_frameshift_variant, eUnknown, GetId(), CVariantPlacement_Base::GetLoc(), CVariantPlacement_Base::GetMol(), CSeq_feat_Base::GetProduct(), CSeq_loc_Base::IsNull(), CSeq_loc_Mapper_Base::Map(), NCBI_THROW, NULL, CRef< C, Locker >::Reset(), SerialClone(), CVariantPlacement_Base::SetExceptions(), CVariantPlacement_Base::SetLoc(), CVariationMethod_Base::SetMethod(), CVariantPlacement_Base::SetMol(), and CSeq_loc::SetWhole().

Referenced by variation::CVariationUtil::TranslateNAtoAA().

Equals()

static bool variation::Equals ( const CVariation::TPlacements &  p1, const CVariation::TPlacements &  p2  )

static

Definition at line 2925 of file variation_util2.cpp.

References CSerialObject::Equals().

Referenced by BOOST_AUTO_TEST_CASE(), CachedTaxonomyLookupCommand(), CCharVectorTypeInfo< Char >::CCharVectorTypeInfo(), ConvertToPairwise(), CPrimitiveTypeInfo::CPrimitiveTypeInfo(), CPrimitiveTypeInfoAnyContent::CPrimitiveTypeInfoAnyContent(), CPrimitiveTypeInfoBitString::CPrimitiveTypeInfoBitString(), CPrimitiveTypeInfoCharPtr< T >::CPrimitiveTypeInfoCharPtr(), CStdTypeInfo< bool >::CreateTypeInfoNullBool(), CTimeTypeInfo::CTimeTypeInfo(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), CGffRecord::GetSubtypeOf(), CBam2Seq_graph::MakeSeq_entry(), variation::CVariationUtil::s_FactorOutPlacements(), SpecificHostCleanupCommand(), TaxonomyLookupCommand(), and CwxChooseSeqDlg::x_GetIdIndex().

FindSSRLoc()

CRef<CSeq_loc> variation::FindSSRLoc	(	const CSeq_loc &	loc,
		const string &	seq,
		CScope &	scope
	)

Definition at line 182 of file hgvs_parser2.cpp.

References CSeq_loc::Assign(), CSeqVector::begin(), CSeq_loc::ChangeToMix(), Compare(), CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Null, CBioseq_Handle::eCoding_Iupac, eExtreme_Positional, eNa_strand_minus, CSeqVector::end(), eNoOverlap, fCompareOverlapping, CSeq_loc::fMerge_SingleRange, CSeq_loc::fSortAndMerge_All, CScope::GetBioseqHandle(), CSeq_interval_Base::GetFrom(), GetId(), CBioseq_Handle::GetInst_Length(), CSeq_loc_Base::GetInt(), CSeqVector::GetSeqData(), GetStrand(), CSeq_interval_Base::GetTo(), HGVS_THROW, i, min(), NULL, result, Seq_loc_Merge(), SeqsMatch(), CSeq_loc::SetInt(), and CSeq_loc::SetMix().

Referenced by variation::CHgvsParser::x_ssr().

GetCommonPrefixLen()

static size_t variation::GetCommonPrefixLen ( const string &  a, const string &  b  )

static

Definition at line 2355 of file variation_util2.cpp.

References a, b, and i.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

GetCommonSuffixLen()

static size_t variation::GetCommonSuffixLen ( const string &  a, const string &  b  )

static

Definition at line 2364 of file variation_util2.cpp.

References a, b, and i.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

GetDelInsSubtype()

CVariation_inst::EType variation::GetDelInsSubtype	(	int	del_len,
		int	ins_len
	)

Definition at line 1277 of file hgvs_parser2.cpp.

References CVariation_inst_Base::eType_del, CVariation_inst_Base::eType_delins, CVariation_inst_Base::eType_ins, CVariation_inst_Base::eType_mnp, and CVariation_inst_Base::eType_snv.

Referenced by variation::CHgvsParser::x_delins(), and variation::CHgvsParser::x_nuc_subst().

GetDeltaLength()

int variation::GetDeltaLength	(	const CDelta_item &	delta,
		int	loc_len
	)

Definition at line 1264 of file hgvs_parser2.cpp.

References delta(), GetLength(), len, and NULL.

Referenced by variation::CHgvsParser::x_delins().

GetFocusLocusIDs()

static set<int> variation::GetFocusLocusIDs ( const CBioseq_Handle &  bsh )

static

Definition at line 3516 of file variation_util2.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Rna, set< Key, Compare >::end(), set< Key, Compare >::find(), CDbtag_Base::GetDb(), CSeq_feat_Handle::GetDbxref(), CSeq_id_Handle::GetHandle(), GetId(), CObject_id_Base::GetId(), CMappedFeat::GetProduct(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CDbtag_Base::GetTag(), SAnnotSelector::IncludeFeatType(), set< Key, Compare >::insert(), IsRefSeqGene(), CSeq_feat_Handle::IsSetDbxref(), CSeq_feat_Handle::IsSetProduct(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, and NULL.

Referenced by variation::CVariationUtil::CVariantPropertiesIndex::x_Index().

GetFuzz()

static const CInt_fuzz* variation::GetFuzz ( const CDelta_item &  delta )

static

Definition at line 4644 of file variation_util2.cpp.

References delta(), and NULL.

Referenced by variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets().

GetFuzzSign()

static int variation::GetFuzzSign ( const CInt_fuzz &  fuzz, int  loc_sign  )

static

Definition at line 174 of file variation_util2.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CInt_fuzz_Base::GetLim(), and CInt_fuzz_Base::IsLim().

Referenced by ValidExonTerminals().

GetSignedOffset()

static int variation::GetSignedOffset ( const CDelta_item &  delta )

static

Definition at line 4638 of file variation_util2.cpp.

References delta().

Referenced by variation::CVariationUtil::s_ConvertInstOffsetsToPlacementOffsets().

GetUniquePrimaryTranscriptId()

CSeq_id_Handle variation::GetUniquePrimaryTranscriptId

(

CBioseq_Handle &

bsh

)

Definition at line 793 of file hgvs_parser2.cpp.

References set< Key, Compare >::begin(), CSeqFeatData_Base::e_Rna, eGetId_ForceAcc, set< Key, Compare >::end(), CSeq_id_Handle::GetHandle(), GetId(), CMappedFeat::GetProduct(), CBioseq_Handle::GetScope(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), SAnnotSelector::IncludeFeatType(), set< Key, Compare >::insert(), CSeq_feat_Handle::IsSetProduct(), CSeq_align_Base::C_Segs::IsSpliced(), and SAnnotSelector::SetResolveTSE().

Referenced by variation::CHgvsParser::x_header().

HasProblematicExceptions()

static bool variation::HasProblematicExceptions ( const CSeq_feat &  cds_feat )

static

Definition at line 2375 of file variation_util2.cpp.

References false, NStr::Find(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), int, CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), NPOS, and true.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

InheritParentAttributes()

CRef<CVariation> variation::InheritParentAttributes	(	const CVariation &	child,
		const CVariation &	parent
	)

Definition at line 4171 of file variation_util2.cpp.

References CVariation_Base::GetId(), CVariation_Base::GetOther_ids(), CVariation_Base::GetParent_id(), CVariation_Base::GetSample_id(), CVariation_Base::IsSetId(), CVariation_Base::IsSetOther_ids(), CVariation_Base::IsSetParent_id(), CVariation_Base::IsSetSample_id(), ITERATE, and SerialClone().

Referenced by variation::CVariationUtil::AsVariation_feats().

IsLRG()

bool variation::IsLRG

(

CBioseq_Handle &

bsh

)

Definition at line 830 of file hgvs_parser2.cpp.

References CBioseq_Handle::GetId(), and ITERATE.

Referenced by variation::CHgvsParser::x_header().

IsMitochondrion()

bool variation::IsMitochondrion

(

CBioseq_Handle

bsh

)

Definition at line 816 of file hgvs_writer2.cpp.

References CBioSource_Base::eGenome_mitochondrion, GetBioSource(), and CBioSource_Base::GetGenome().

Referenced by variation::CHgvsParser::x_AsHgvsInstExpression().

IsPureFuzzPoint()

bool variation::IsPureFuzzPoint

(

const CSeq_point &

p

)

Definition at line 566 of file hgvs_parser2.cpp.

References CInt_fuzz_Base::eLim_other, CSeq_point_Base::GetFuzz(), CInt_fuzz_Base::GetLim(), CSeq_point_Base::GetPoint(), CInt_fuzz_Base::IsLim(), CSeq_point_Base::IsSetFuzz(), and kInvalidSeqPos.

Referenced by variation::CHgvsParser::x_fuzzy_pos(), and variation::CHgvsParser::x_general_pos().

IsRefSeqGene()

static bool variation::IsRefSeqGene ( const CBioseq_Handle &  bsh )

static

Definition at line 3495 of file variation_util2.cpp.

References CBioseq_Handle::CanGetDescr(), CSeq_descr_Base::Get(), CBioseq_Handle::GetDescr(), CSeqdesc_Base::GetGenbank(), CGB_block_Base::GetKeywords(), CSeqdesc_Base::IsGenbank(), and ITERATE.

Referenced by GetFocusLocusIDs().

IsRightPartial()

static bool variation::IsRightPartial ( CBioseq_Handle  bsh )

static

Definition at line 1623 of file variation_util2.cpp.

References CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_right, CSeq_descr_Base::Get(), CMolInfo_Base::GetCompleteness(), CBioseq_Handle::GetDescr(), CSeqdesc_Base::GetMolinfo(), CSeqdesc_Base::IsMolinfo(), CMolInfo_Base::IsSetCompleteness(), and ITERATE.

Referenced by variation::CVariationUtil::x_GetLiteralAtLoc().

Ncbieaa2HgvsAA()

string variation::Ncbieaa2HgvsAA

(

const string &

prot_str

)

Definition at line 403 of file hgvs_writer2.cpp.

References CTempString::find(), i, NPOS, out(), and CTempString::substr().

Referenced by variation::CHgvsParser::x_PlacementCoordsToStr(), and variation::CHgvsParser::x_SeqLiteralToStr().

RepackageAssertedSequence()

void variation::RepackageAssertedSequence

(

CVariation &

vr

)

Definition at line 299 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), delta(), CVariation_Base::C_Data::C_Set::eData_set_type_package, CVariation_inst_Base::eObservation_asserted, CVariation_inst_Base::eType_identity, CVariation_Base::GetData(), CVariation_Base::C_Data::IsSet(), CVariation_Base::IsSetPlacements(), NON_CONST_ITERATE, orig, CVariantPlacement_Base::ResetSeq(), CVariation_Base::SetData(), SetFirstPlacement(), and CVariation_Base::SetPlacements().

Referenced by variation::CHgvsParser::x_root().

SeqsMatch()

bool variation::SeqsMatch	(	const string &	query,
		const char *	text
	)

Definition at line 168 of file hgvs_parser2.cpp.

References a, b, CTempString::find(), i, query, and text().

Referenced by FindSSRLoc().

SetComputational()

void variation::SetComputational

(

CVariation &

variation

)

Definition at line 154 of file hgvs_parser2.cpp.

References CVariationMethod_Base::eMethod_E_computational, CVariationMethod_Base::GetMethod(), and CVariationMethod_Base::SetMethod().

Referenced by variation::CHgvsParser::x_expr1(), variation::CHgvsParser::x_expr2(), and variation::CHgvsParser::x_expr3().

SetFirstPlacement()

CVariantPlacement& variation::SetFirstPlacement

(

CVariation &

v

)

Definition at line 145 of file hgvs_parser2.cpp.

References CVariation_Base::SetPlacements().

Referenced by RepackageAssertedSequence(), variation::CHgvsParser::x_conversion(), variation::CHgvsParser::x_deletion(), variation::CHgvsParser::x_delins(), variation::CHgvsParser::x_duplication(), variation::CHgvsParser::x_expr2(), variation::CHgvsParser::x_insertion(), variation::CHgvsParser::x_mut_inst(), variation::CHgvsParser::x_no_change(), variation::CHgvsParser::x_nuc_inv(), variation::CHgvsParser::x_nuc_subst(), variation::CHgvsParser::x_prot_ext(), variation::CHgvsParser::x_prot_fs(), variation::CHgvsParser::x_prot_missense(), variation::CHgvsParser::x_ssr(), variation::CHgvsParser::x_string_content(), and variation::CHgvsParser::x_translocation().

SwapLtGtFuzz()

static void variation::SwapLtGtFuzz ( CInt_fuzz &  fuzz )

static

Definition at line 292 of file variation_util2.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::IsLim(), and CInt_fuzz_Base::SetLim().

Referenced by ApplyOffsetFuzz().

Translate()

static string variation::Translate ( const string &  nuc_str, bool  is_mito  )

static

Definition at line 1971 of file variation_util2.cpp.

References CSeqTranslator::fIs5PrimePartial, NPOS, and CSeqTranslator::Translate().

Referenced by variation::CVariationUtil::TranslateNAtoAA().

USING_SCOPE()

variation::USING_SCOPE

(

objects

)

ValidExonTerminal()

static bool variation::ValidExonTerminal ( const set< TSeqPos > &  exon_biostarts, const set< TSeqPos > &  exon_biostops, TSeqPos  exon_anchor_pos, int  offset_pos  )

static

Definition at line 152 of file variation_util2.cpp.

References set< Key, Compare >::end(), and set< Key, Compare >::find().

Referenced by ValidExonTerminals().

ValidExonTerminals()

static bool variation::ValidExonTerminals ( const set< TSeqPos > &  exon_biostarts, const set< TSeqPos > &  exon_biostops, const CVariantPlacement &  p  )

static

Definition at line 185 of file variation_util2.cpp.

References eExtreme_Biological, eNa_strand_minus, GetFuzzSign(), CVariantPlacement_Base::GetLoc(), GetStart(), CVariantPlacement_Base::GetStart_offset(), CVariantPlacement_Base::GetStart_offset_fuzz(), GetStop(), CVariantPlacement_Base::GetStop_offset(), CVariantPlacement_Base::GetStop_offset_fuzz(), GetStrand(), CVariantPlacement_Base::IsSetStart_offset(), CVariantPlacement_Base::IsSetStart_offset_fuzz(), CVariantPlacement_Base::IsSetStop_offset(), CVariantPlacement_Base::IsSetStop_offset_fuzz(), NULL, and ValidExonTerminal().

Referenced by variation::CVariationUtil::CheckExonBoundary().